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Niema Moshiri - Ph.D. Candidate
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Niema Moshiri

Ph.D. Candidate
University of California System • University of California, San Diego • San Diego • United States of America

Skills and expertise

Fields of interest
  • WGS analysis
  • De novo sequencing analysis
  • RNA-seq analysis
Languages
  • English
Programming languages
  • C
  • C++
  • Java
  • MATLAB
  • Python
  • R
  • Shell (Bash)

Favorites and Collections

Favorites

TreeCluster
Desktop
FAVITES
Desktop

Collections

No collections...

Bioinformatics projects

TOOLS MAINTAINED

TreeN93

Desktop

TreeN93

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Provides a threshold-free distance-based tool for inferring viral transmission clusters. TreeN93 proceeds by executing transmission cluster identification from pairwise TN93 distances. This software…
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TreeSwift

Desktop

TreeSwift

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Assists users in traversing and manipulating trees. TreeSwift is a package that consists of two classes: (i) a Node class, which contains the data and local relationships, and (ii) a Tree class,…

TreeCluster

Desktop

TreeCluster

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Deduces transmission clusters from a given phylogenetic tree inferred from viral sequences. TreeCluster reduces the number of clusters of leaves of a bifurcating phylogenetic tree through several…

Education

Ph.D. Bioinformatics and Systems Biology
University of California, San Diego
2015 - Today
B.S. Bioengineering: Bioinformatics (Minor in Economics)
University of California, San Diego
2011 - 2015

Fields of interest

WGS analysis
Assists in small-variant detection. Pisces is designed to be used on germline…
Allows the joint analysis of individual-level data and summary statistics. LEP…
Allows annotation and prediction of cis-expression quantitative trait locus…
De novo sequencing analysis
Assists in small-variant detection. Pisces is designed to be used on germline…
Represents all sequence reads and their similarity relationships using a graph…
Discovers large indels using optical maps (OM) reads with weak signal. OMIndel…
RNA-seq analysis
Identifies protein-lncRNA interactions. PLIPCOM is constructed from three…
Discovers large indels using optical maps (OM) reads with weak signal. OMIndel…
Identifies genetic variants that overlap with genes coding for lincRNA or miRNA…